The Roles of Conserved Carboxylate Residues in IMP

The Roles of Conserved Carboxylate Residues in IMP Dehydrogenase and. Identification of a Transition State Analog†. Kathleen M. Kerr and Lizbeth Hed...
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Biochemistry 1997, 36, 13365-13373

13365

The Roles of Conserved Carboxylate Residues in IMP Dehydrogenase and Identification of a Transition State Analog† Kathleen M. Kerr and Lizbeth Hedstrom* Department of Biochemistry, Brandeis UniVersity, Waltham, Massachusetts 02254 ReceiVed June 12, 1997; ReVised Manuscript ReceiVed August 28, 1997X

ABSTRACT:

IMP dehydrogenase (IMPDH) catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+; the enzyme is activated by K+. This reaction is the rate-limiting step in de noVo guanine nucleotide biosynthesis. In order to identify functionally important residues in IMPDH, including those involved in substrate and K+ binding, we have mutated 11 conserved Asp and Glu residues to Ala in Escherichia coli IMPDH. The values of kcat, Km, and Ki for GMP, XMP, mizoribine 5′-monophosphate (MMP), and β-methylene-tiazofurin adenine dinucleotide (TAD) were determined. Five of these mutations caused a significant change (g10-fold) in one of these parameters. The Asp248 f Ala mutation caused 100-fold decrease in the value of kcat and a 25-fold increase in the value of Kii for TAD; these observations suggest that Asp248 is in the NAD+ binding site. The Asp338 f Ala mutation caused a 600-fold decrease in the value of kcat, but only a 5-10-fold increase in the values of Km for IMP and Kis for IMP analogs, suggesting that Asp338 may be involved in acid-base catalysis as well as IMP binding. The remaining three residues, Asp13, Asp50, and Glu469, appear to be involved in K+ activation; these residues may be ligands at one or more K+ binding sites. Interestingly, changes in the values of Ki for MMP correlate with changes in kcat/KmKm of IMPDH, while no such correlation is observed for GMP, XMP, and TAD. This observation indicates that MMP is a transition state analog for the IMPDH reaction.

IMP dehydrogenase (IMPDH)1 catalyzes the oxidation of IMP to XMP with the conversion of NAD+ to NADH. This reaction controls the overall rate of de noVo guanine nucleotide biosynthesis. Guanine nucleotides play a central role in cell growth processes, such as DNA and RNA biosynthesis, signal transduction, and tubulin assembly. Thus, IMPDH activity regulates cellular guanine levels and consequently affects cell proliferation (Weber, 1983). IMPDH inhibitors target rapidly proliferating cells and are potential therapeutics for cancer. Furthermore, IMPDH inhibitors ribavarin, mizoribine, and mycophenolate mofetil are currently used in antiviral and immunosuppressive therapies (Streeter et al., 1973; Robins, 1982; Allison, 1993). In addition, mammalian and microbial IMPDHs differ significantly in inhibitor sensitivity and catalytic efficiency, which suggests that IMPDH may be a target for anti-infective agents (Hupe et al., 1986; Verham et al., 1987; Wang et al., 1996). Overall, the potential therapeutic benefits from the investigation of the mechanism of IMPDH are clear. Our goal is to define functionally important residues in IMPDH. † Funded by NIH Molecular Structure and Function Training Grant GM07956 (K.M.K.) and a grant from the Lucille P. Markey Charitable Trust to Brandeis University. L.H. is a Searle Scholar and a Beckman Young Investigator. This manuscript is No. 1817 from the Department of Biochemistry, Brandeis University. * To whom correspondence should be addressed. X Abstract published in AdVance ACS Abstracts, October 15, 1997. 1 Abbreviations: IMPDH, inosine 5′-monophosphate dehydrogenase; IMP, inosine 5′-monophosphate; NAD+, nicotinamide adenine dinucleotide; NADH, reduced nicotinamide adenine dinucleotide; XMP, xanthosine 5′-monophosphate; GMP, guanosine 5′-monophosphate; MPA, mycophenolic acid; TAD, β-methylene tiazofurin adenine dinucleotide; MMP, mizoribine 5′-monophosphate; EDC, 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide; EICARMP, 5-ethynyl-1-β-D-ribofuranosylimidazole-4-carboxamide 5′-monophosphate; DTT, dithiothreitol; PAGE, polyacrylamide gel electrophoresis.

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A mechanism for the IMPDH reaction is shown in Figure 1. The reaction is initiated by the attack of Cys305 (Escherichia coli IMPDH numbering) on the 2 position of IMP forming a covalent E-IMP intermediate. In the subsequent step, hydride is transferred to NAD+ producing NADH and an E-XMP* intermediate (Huete-Perez et al., 1995; Link & Straub, 1996; Sintchak et al., 1996). This intermediate is hydrolyzed to release XMP and regenerate the free enzyme. Two general acid-base catalysts are expected to be involved in the IMPDH mechanism: a general acid stabilizes the tetrahedral intermediates formed by the attack of Cys305 on IMP and by the attack of water on E-XMP* and a general base catalyst activates water. These residues have not been identified. IMPDH is activated by monovalent cations. The extent of activation and cation specificity vary among IMPDHs from different sources (Anderson & Sartorelli, 1968; Powell et al., 1969; Heyde et al., 1976; Atkins et al., 1985; Xiang et al., 1996; Verham et al., 1987). K+ is the most effective activator. E. coli IMPDH activity increases 100-fold in the presence of K+, while only a 10-fold increase is observed in the activity of Tritrichomonas foetus (Verham et al., 1987; J. Digits and L. Hedstrom, unpublished observations). In general, larger cations, such as Rb+, NH4+, and Cs+, also activate IMPDH while smaller cations, such as Li+ and Na+, inhibit. The mechanism of monovalent cation activation of IMPDH is not understood: the stoichiometry of K+ binding to IMPDH has not been determined nor have the ligands of the K+ binding site(s) been identified. Since active site residues are generally conserved throughout evolution, sequence alignments can provide clues to functionally important residues. Amino acid sequences are presently available for IMPDHs from 25 sources, including archae, eubacteria, and eukaryote organisms. Carboxylate © 1997 American Chemical Society

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FIGURE 1: Mechanism of the IMPDH reaction. Table 1: Conserved Carboxylate Residues in IMPDHa residue classification

speciesb

archae bacteria

Methanococcus jannaschii Pyrococcus furiosus Myobacterium leprae Myobacterium tuberculosis Bacillus subtilis Escherichia coli Streptococcus pyogenes Haemophilus influenzae Acinetobacter calcoaceticus Borrelia burgdorferi Leishmania donoVani Trypanosoma brucei brucei Saccharomyces cereVisiae XII Saccharomyces cereVisiae VIII Saccharomyces cereVisiae XIII Mus musculus a Mus musculus b Cricetulus griseus Homo sapiens type 1 Homo sapiens type 2 Mus musculus type 1 Drosophila melanogaster Pneumocystis carinii Arabidopsis thaliana Tritrichomonas foetus

eubacteria

eukaryotae

13 (34)

50 (71)

54 (75)

138 (162)

200 (226)

243 (269)

248 (274)

293 (319)

338 (364)

369 (395)

373 (399)

469 (500)

D D D D D D D D D D D D D D D D D D D D D D

D D D D D D D D D D D D D D D D D D D D D D D D Q

E E E E E E G E E E E E E E E E E E E E E E E E G

D D D D D D D D D T D D D D D D D D D D D D D Q D

D D D D D D D D D N D D D D D D D D D D D D D D D

D D D D D D D D D D D D D D D D D D D D D D D N D

D D D D D D D D D D D D D D D D D D D D D D D D D

D

D D D D D D D D D D D D D D D D D D D D D D D D D

E E E E E E E E E E E E E E E E E E E E E E E E E

G K E E E E E E E E E E E E E E E E E E E E Q G R

E E E E E E E E E E E E E E E E E E E E E E E E E

D E

D D D S S D D D D D D D D D D D D D D D D D D

a Sequences of 25 IMPDH proteins from various sources were compiled from a BLAST search of the National Center for Biological Information (NCBI) database using E. coli as the template. The sequences were aligned using PILEUP in the GCG software package, and carboxylate residues with g80% identity are shown. Numbering denotes the residue in the E. coli sequence, and the parentheses denote the corresponding residue number in the human type 2 sequence. b Species (NCBI identification number): M. jannaschii (1592337), P. furiosus (1170554), M. leprae (466944), M. tuberculosis (1449376), B. subtilis (124423), S. pyogenes (924848), E. coli (729847), H. influenzae (1170553), A. calcoaceticus (400057), B. burgdorferi (1352459), L. donoVani (124425), T. brucei brucei (1078708), S. cereVisiae XII (665971), S. cereVisiae VIII (729848), S. cereVisiae XIII (577140), M. musculus a (425158), M. musculus b (124427), C. griseus (304517), H. sapiens type 1 (124417), H. sapiens type 2 (124419), M. musculus type 1 (392948), D. melanogaster (1170552), P. carinii (1272244), A. thaliana (1352458), T. foetus (1352865).

residues are the largest class of conserved residues among IMPDHs (Table 1), and several roles for carboxylate residues can be envisioned. Asp and Glu residues can act as general acids and/or bases, as shown in the mechanism in Figure 1. In addition, carboxylate residues are commonly involved in binding sites of nucleotides and nicotinamide cofactors (Montfort et al., 1990; Betts et al., 1994; Bellamacina, 1996). Carboxylate residues are also found in K+ binding sites (Toney et al., 1993; Larsen et al., 1994; Liaw et al., 1995; Koster et al., 1996). Therefore, Asp and Glu residues emerge as good candidates for functionally important residues of IMPDH.

Here, an alanine scanning study investigates the roles of conserved Asp and Glu residues in E. coli IMPDH. We have identified five functionally important Asp/Glu residues. In addition, we have found that mizoribine 5′-monophosphate (MMP) is a transition state analog inhibitor of the IMPDH reaction (Figure 2). While this work was in progress, crystal structures for IMPDH from Chinese hamster and T. foetus were solved (Sintchak et al., 1996; Whitby et al., 1997). Since the coordinates of the T. foetus structure have only recently become available (and the hamster structure coordinates are not yet released), we will compare our results with the current structural information in the Discussion.

Conserved Carboxylate Residues in IMPDH

FIGURE 2: Mizoribine 5′-monophosphate (MMP) (left) and β-CH2tiazofurin adenine dinucleotide (TAD) (right).

MATERIALS AND METHODS Materials. IMP, NAD+ , XMP, and GMP were purchased from Sigma; glycerin was purchased from Fisher. The plasmid pJS49 containing the E. coli guaB gene was the gift of Dr. John M. Smith (Teideman & Smith, 1985). The p1 transducing lysate of p1-AB1157 and a recA-deficient donor strain STL134 were provided by Dr. Susan Lovett. MMP and EICARMP were the gift of Dr. Akira Matsuda, and TAD was the gift of Dr. Victor Marquez. Mutagenesis. Asp54Ala, Asp138Ala, Asp243Ala, Glu373Ala, and Glu469Ala were constructed from pJS49 using the Quikchange kit (Stratagene, La Jolla, CA). The E. coli guaB gene was subcloned from pJS49 into pBluescriptKS+ in order to construct Asp13Ala, Asp50Ala, Asp200Ala, Asp248Ala, Asp338Ala, and Glu369Ala using Kunkel mutagenesis (Kunkel, 1985). To ensure no undesired mutations had been introduced, the coding sequences of all IMPDH genes were sequenced using a PRISM Dyedeoxy Terminator Cycle Sequencing kit (Applied Biosystems, Inc.) and an Applied Biosystems 373A DNA sequencer at the Brandeis Sequencing Facility. LH3 Strain Construction. A recombination-deficient strain of H712 was made using a p1 transducing lysate method (Miller, 1992). The donor strain (STL143, recA∆306::Tn10) truncated the recA gene in the H712 genome with a tetracycline resistance gene. The new cell strain, LH3, showed an IMPDH-deficient, recombination-deficient phenotype (genotype, F-fhuA2 lacY1 tsx-70 supE44? gal-6 λtrp-45 his-68 guaB22 tyrA2 rspL125 malT1(λR) xyl-7 mtl-2 thi-1 recA∆306::Tn10). Expression of IMPDH. Plasmids containing a wild-type or mutant IMPDH gene were transformed into LH3 cells using the TSS quick transformation method (Chung et al., 1989). Cells were grown for 48 h in 1.2 L LB broth with 100 µg/mL ampicillin and 20 µg/ml tetracycline at 37 °C with constant agitation. Purification of IMPDH. Wild-type and mutant IMPDHs were purified by similar methods. The cells were harvested and washed three times with 50 mM Tris, pH 7.5, 1 mM DTT, and 10% glycerol (buffer A) and resuspended in 40 mL of buffer A and frozen at -80 °C. IMPDH was purified as previously described (Farazi et al., 1997) with the following modifications: a linear gradient of 0 to 2 M KCl was used to elute the protein from the Cibacron Blue Sepharose resin (Sigma) and a linear gradient of 0 to 1 M NaCl was used to elute the protein from the POROS CM Weak Cation Exchange column (PerSeptive Biosystems, Framingham, MA). Fractions containing IMPDH were pooled according to activity (wild-type) or SDS-PAGE (mutants). Enzyme was dialyzed against buffer A and stored

Biochemistry, Vol. 36, No. 43, 1997 13367 at -80 °C. The enzyme preparations were judged >90% homogenous by SDS-PAGE stained with Coomassie Blue. ActiVe Site Titration. Protein concentrations for wild-type and all mutants except Asp338Ala were determined by active site titration with EICARMP (Wang et al., 1996). EICARMP does not inactivate Asp338Ala stoichiometrically; therefore, the concentration of Asp338Ala was determined using the Bio-Rad assay (IgG standard) calibrated from similar preparations of wild-type IMPDH. NatiVe Gel Electrophoresis. Wild-type and mutant proteins were subjected to native polyacrylamide gel electrophoresis to probe quaternary structure. A gel [7 in. (width) × 8 in. (length)] was prepared with 5% acrylamide (2.6% cross-linked) and 50 mM Tris, pH 8.0 and polymerized with 0.04% ammonium persulfate and 0.08% TEMED. Approximately 10 µg of each protein was loaded, and the gel was run at 95 V for 10 h at 4 °C in 50 mM Tris, pH 8.0, running buffer with three buffer changes. The gel was stained with Coomassie Blue to visualize the protein. Enzyme Assays. Standard E. coli IMPDH activity assays contained 50 mM Tris, pH 8.0, 100 mM KCl, 3 mM EDTA, 1 mM DTT, 1 mM IMP, and 2.5 mM NAD+. The reaction was initiated by the addition of enzyme, and the production of NADH (340 ) 6.2 mM-1 cm-1) was monitored at 25 °C using an Hitachi U-2000 spectrophotometer. To detect the activity of Asp338Ala, the production of NADH was monitored by fluorescence (excitation λ, 340 nm; emission λ, 460 nm) at 25 °C using either an Hitachi F-2000 fluorescence spectrophotometer or a PerSeptive Biosystems Cytofluor II multiwell plate reader. Concentrations of IMP and NAD+ were varied appropriately for all wild-type and mutant Km determinations. EDC InactiVation. Wild-type IMPDH was incubated in 50 mM Tris, pH 7.5, 10% glycerol, and 1 mM DTT at 25oC with 10 mM EDC, in the presence and absence of ethanolamine, and in the presence and absence of IMP. Controls contained no EDC. Aliquots were removed at appropriate times and assayed for enzymatic activity as described above. Rates of inactivation (kinact) were determined from the slopes of semilogarithmic plots of the fraction activity vs incubation time. Data Analysis. Michaelis-Menten parameters for wildtype and mutant IMPDHs were determined by fitting initial rate data to the Michaelis-Menten equation (1) and substrate inhibition equation (2):

υ/E ) kcatA/(Ka + A)

(1)

υ/E ) kcatB/(Kb + B + B2/Kii)

(2)

where υ/E is the initial velocity, kcat is the overall rate constant, A is the IMP concentration, Ka is the MichaelisMenten constant for IMP, B is the NAD+ concentration, Kb is the Michaelis-Menten constant for NAD+, and Kii is the substrate inhibition constant for NAD+. Steady state parameters with respect to NAD+ were derived by first determining apparent kcat values for the initial velocity vs IMP (eq 1) then replotting these values vs NAD+ concentration (eq 2), resulting in the determination of Kb, Kii, and kcat. Similarly, the steady state parameters with respect to IMP were derived using the apparent kcat values for the initial velocity vs NAD+ (eq 2), then replotting vs IMP concentration (eq 1) resulting in determination of Ka

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and kcat. The average of the kcat values was reported. The initial rate data from Asp13Ala, Asp50Ala, Asp248Ala, and Asp338Ala could not be fit to eq 2; the steady state parameters of these mutants were determined using eq 3 for sequential mechanism:

υ/E ) kcatAB/(KiaKb + KaB + KbA + AB)

(3)

where Kia is the dissociation constant for IMP from the binary E‚A complex. Wild-type and all mutant enzyme activities were assayed at saturating IMP and NAD+ concentrations and varied K+ concentrations, and initial rate data were fit to eq 4:

υ/E ) kcat[K+]/(Km + [K+]) + C

(4)

where Km is the apparent Michaelis-Menten constant of K+ and C is a constant. All further characterization of Michaelis-Menten parameters and inhibition constants of Asp13Ala, Asp50Ala, and Glu469Ala was performed with 400 mM KCl in the assay buffer. Inhibitor Analysis. For GMP and XMP, the values of Kis were determined with constant NAD+ concentrations and varied IMP and inhibitor concentrations. Initial rate data were fit to eq 5 for competitive inhibition:

υ/E ) kcatA/[Ka(1 + I/Kis) + A]

(5)

where I is the concentration of the inhibitor and Kis is the dissociation constant of the E‚I complex. For TAD, the values of Kii were determined with constant IMP concentrations and varied NAD+ and TAD concentrations. Initial rate data were fit to eq 6 for uncompetitive inhibition:

υ/E ) kcatB/[Kb + B(1 + I/Kii)]

(6)

where Kii is the inhibition constant for TAD. For MMP, the values of Ki were determined using tight binding inhibitor and progress curve analysis. For tight binding inhibition, the values of Ki were determined with constant NAD+ concentrations and varied IMP and MMP concentrations. Initial rate data were fit to the Ackermann equation for competitive inhibition (eq 7) (Ackermann & Potter, 1949):

υ ) (kcat/2)(E - KiQ - 1) + [(KiQ + I + E)2 - 4IE]0.5 (7) where υ is the initial velocity, E is the concentration of IMPDH active sites, and Q is [1 + (A/Ka)]. Progress curve analysis was used when time-dependent inhibition was observed. The IMP and NAD+ concentrations were constant while the MMP concentration was varied, and the reaction was monitored for 60 min. Data were analyzed by fitting to eqs 8, 9, and 10 (Orsi & Tipton, 1979; Hager et al., 1995):

υ/E ) (koffkcat/b)t +(Ikon′kcat/b2)(1 - e-bt)

(8)

kon ) kon′Q

(9)

Ki ) koff/kon

(10)

where koff is the dissociation rate constant of the E‚I complex, b ) (Ikon′ + koff), t is time, and kon′ is the apparent association

FIGURE 3: EDC inactivation and partial IMP protection of IMPDH. (A) E. coli IMPDH, 1.4 µM, was incubated with 10 mM EDC and various concentrations of ethanolamine, [RNH2] ) 0 (∆), 50 (ο), and 100 mM ()), and enzyme activity was measured at appropriate intervals as described in Materials and Methods. Control (b) contained no EDC. (B) E. coli IMPDH, 1.4 µM, was incubated with 10 mM EDC, 100 mM ethanolamine, and varied concentrations of IMP. kinact was determined as described in Materials and Methods.

rate constant of the E‚I complex. All data were fit to the appropriate equations using either KinetAsyst, Kaleidagraph, or Sigma Plot software. RESULTS EDC InactiVation of IMPDH. We tested the ability of carbodiimide reagents to inactivate IMPDH in order to provide evidence for the involvement of a carboxylate residue in the IMPDH reaction. Carbodiimide modification is commonly used to cross-link proteins and to identify exposed nucleophillic residues in proteins (Carraway & Koshland, 1972). Carbodiimide-modified carboxylate residues further react with amines to form amides; this reaction is diagnostic for the modification of carboxylates. IMPDH is inactivated by the carbodiimide EDC (Figure 3A). This inactivation is not caused by protein cross-linking as determined by SDSPAGE of inactivated protein (data not shown). The rate of inactivation increases in the presence of ethanolamine (Figure 3A), which indicates that EDC inactivates IMPDH by modifying Asp and/or Glu residue(s). IMP partially protects IMPDH from EDC inactivation (Figure 3B). This observation indicates that EDC modifies a carboxylate residue outside the IMP binding site, perhaps in the NAD+ or K+ binding sites. In addition, since IMP protects IMPDH from inactivation by thiol reagents, this observation provides further evidence that EDC inactivation does not result from modification of the active site Cys (Brox & Hampton, 1968; Antonino et al., 1994; Huete-Perez et al., 1995). Thus, the

Conserved Carboxylate Residues in IMPDH

FIGURE 4: Native polyacrylamide gel of wild-type and mutant proteins. Each protein (10 µg) was analyzed on a 5% polyacrylamide gel at 4 °C as described in Materials and Methods.

inactivation of IMPDH by EDC suggests that a carboxylate residue is required in the IMPDH reaction. ConserVed Carboxylates in E. Coli IMPDH. Twelve Asp and Glu residues are conserved among IMPDHs from various sources (Table 1). Four of these residues, Asp248, Asp338, Glu369, and Glu469, are fully conserved. An additional three residues, Asp50, Asp200, and Asp243, are conserved in 24 of 25 sequences, and another three, Asp13, Asp54, and Asp138, are conserved in 23 of the sequences. It seemed prudent to include these 10 residues in the alanine scanning study. In addition, residue 373 was also included at the initiation of this study; the report of additional IMPDH sequences showed that this residue is conserved in only 20 of 25 sequences. Residue 293 is a Ser in E. coli and was therefore omitted from this study. Expression of IMPDH Mutants. The E. coli strain H712 is commonly used to express recombinant IMPDH protein (Antonino & Wu, 1994; Farazi et al, 1997; Xiang et al., 1996; Sintchak et al., 1996). This strain lacks endogenous IMPDH activity, and H712 cells do not grow on minimal media in the absence of guanine (Nijkamp & De Haan, 1967). However, when these cells were transformed with a plasmid carrying an inactive E. coli IMPDH gene (Cys305 f Ala mutation), the transformants grew on minimal media. This observation suggests that recombination had occurred between the plasmid and chromosomal IMPDH genes regenerating a wild-type gene. Therefore, a recombinationdeficient strain of H712, LH3, was constructed. LH3 cells transformed with a Cys305Ala IMPDH gene do not grow on minimal media. All mutant IMPDHs were expressed in LH3 cells. Interestingly, less active IMPDH mutants are expressed in greater quantities than wild-type IMPDH. All IMPDH mutants were purified using standard procedures as described in Materials and Methods. Quaternary Structure of the IMPDH Mutants. The smallest active oligomer of E. coli IMPDH is a tetramer, although higher order enzyme aggregates are also formed (Powell, 1973; Gilbert et al., 1979). We analyzed the quaternary structure of the mutant IMPDHs by native PAGE (Figure 4). Both size and charge determine the migration of proteins in native PAGE (Hames & Rickwood, 1990), and this method can easily distinguish monomers from dimers and

Biochemistry, Vol. 36, No. 43, 1997 13369 tetramers [see, for example, Maley et al. (1995)]. Wildtype IMPDH displayed multiple bands, as expected for an aggregating protein. The smallest molecular weight band migrated similar to catalase (Mm ) 240 kDa), which is consistent with the molecular mass of a tetramer of E. coli IMPDH (Mm ) 220 kDa) (data not shown). Like the wildtype enzyme, all of the mutant enzymes display multiple bands. The mobility of the smallest molecular mass band in the mutant enzymes is the same as wild-type in all cases, which indicates all of the mutant enzymes form tetramers. No faster migrating bands are observed for any of the mutant enzymes, further indicating that no monomeric or dimeric forms are observed in the mutants. The ability to form tetramers, and the failure to observe monomers or dimers, indicates that the mutations do not grossly perturb the structure of IMPDH. Interestingly, all of the mutant enzymes form higher order aggregate species similar to wild-type, although the aggregation pattern of Asp243Ala differs from the other proteins. ActiVity of Wild-Type E. coli IMPDH. Table 2 summarizes the Michaelis-Menten parameters for wild-type IMPDH, as well as the values of Ki for inhibition by IMP analogs XMP, GMP, and MMP and the NAD+ analog TAD (Figure 2). Like IMPDH from other organisms, substrate inhibition is observed at high concentrations of NAD+ for E. coli IMPDH (Hedstrom & Wang, 1990; Zhou et al, 1997; Xiang & Markham, 1996) (Figure 5). Presumably, this inhibition results from NAD+ binding to the E-XMP* intermediate (Wu et al., 1995). No IMP substrate inhibition is observed. The values of kcat, Km, and Ki for wild-type IMPDH are similar to those reported although previous characterizations of E. coli IMPDH did not account for NAD+ substrate inhibition (Table 2) [Km (IMP) ) 11 µM, Km (NAD+) ) 330 µM, Ki (GMP) ) 56 µM, (Gilbert et al., 1979); Km (IMP) ) 13 µM, Km (NAD+) ) 190 µM, Ki (GMP) ) 82 µM, Ki (XMP) ) 130 µM (Powell et al., 1969)]. IMPDH is activated 100fold in the presence of K+, with an apparent Km for K+ ) 2.8 mM. Interestingly, MMP is a more potent inhibitor of E. coli IMPDH than mammalian IMPDHs [Ki ) 0.5 nM for E. coli (Table 2) versus Ki ) 4 nM for human IMPDH type II (Hager et al., 1995)], although TAD is a less potent inhibitor [Kii ) 8.5 µM for E. coli versus Ki ) 0.2 µM for mouse IMPDH (Marquez et al, 1986)]. ActiVity of the IMPDH Mutants. Six mutants, Glu54Ala, Asp138Ala, Asp200Ala, Asp243Ala, Glu369Ala, and Glu373Ala, show no significant changes with respect to wildtype in all parameters assayed (Table 2). At least one parameter is changed by g10-fold in the remaining five mutants, Asp13Ala, Asp50Ala, Asp248Ala, Asp338Ala, and Glu469Ala. Surprisingly, the mutations have the greatest effect on the value of Ki for MMP except in the case of Asp248Ala. The significance of this observation will be discussed below. The effects of the mutations on the other parameters are summarized as follows. Asp13Ala. The Asp13 f Ala mutation causes a 38-fold increase in the value of Km for K+. This mutation also decreases the value of kcat by 19-fold. No change is observed in the value of Km for IMP or in the values of Kis for GMP and XMP. Unlike the other IMP analogs, the value of Kis for MMP increases by 60-fold. While the Km for NAD+ increases by 3-fold, the value of Kii for TAD is unchanged. No NAD+ substrate inhibition is detected, which may signal a decrease in the accumulation of E-XMP* and is in keeping

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Table 2: Kinetic Charaterization of E. coli IMPDH and Mutants (Unless Otherwise Noted, Error Was e15%) enzyme

kcat s-1

kcat/KmKm [(sM2)-1 × 107]

Km IMP (µM)

Km NAD+ (mM)

Kii NAD+ (mM)

K m K+ (mM)

Kis GMP (µM)

Kis XMP (µM)

Ki MMP (nM)

Kii TAD (µM)

wild-type D13Ab D50Ab E54A D138A D200A D243A D248A D338A E369A E373A E469Ab

13 0.7 1.2 14 7.1 14 12 0.1a 0.02a 7.1 7.1 14

11 0.23 0.48 6.7 12 21 11 0.08 0.0009 6.7 7.5 2.6

61 52a 61a 87a 44a 44 56a 21a 710a 53a 59 49

2.0a 5.7 4.1a 2.4 1.4 1.5 2.0 6.3a 3.3a 2.0 1.6a 11

2.8 na na 3.6 4.5 5.6 7.5 nae na 5.5 4.3 3.6

2.8 107 48 6.0 4.3 5.2 4.0 35 17 7.2 5.3 48

86a 160 670 230 78 150 88 64 510 300 93 160

130 240 930 230 72 130 120 30a 600a 340 110 130a

0.5c 30a,d 60a,d 1.8a,c 1.1a,c 0.4a,c 0.7c 40a,d 700d 1.9a,c 0.6a,c 0.8c

8.5 5.6 1.7 ndf nd nd nd 210a nd nd nd 8.4a

a Error was e25%. b Kinetic constants determined at 400 mM KCl. cProgress curve analysis. dTight binding analysis. ena, not applicable. end, not done.

FIGURE 5: NAD+ substrate inhibition. Enzyme activity was assayed with 50 mM Tris, pH 8.0, 400 mM KCl, 3 mM EDTA, 1 mM DTT, and 1 mM IMP (wild-type contained 100 mM KCl). The values of the initial rates of NADH formation by wild-type (b) and Glu469Ala ([) (left axis) were fit to eq 2, which describes substrate inhibition. The values of the initial rates of NADH formation by Asp13Ala (4) (right axis) were fit to eq 1 for Michaelis-Menten kinetics.

with the decrease in the value of kcat (Figure 5). Since large changes are observed in K+ affinity and kcat, we suggest that Asp13 is involved in K+ activation and may be a ligand at the K+ binding site. Asp50Ala. The Asp50 f Ala mutation also causes an 17fold increase in the value of Km for K+ and 10-fold decrease in the value of kcat. Interestingly, Asp50Ala exhibits sigmoidal kinetics at a low concentration of K+, although Michaelis-Menten kinetics are observed at high K+ concentrations (data not shown). This mutation has wide ranging and apparently contradictory effects. For example, while no change in the value of Km for IMP is observed, the values of Kis for GMP and XMP increase by 7-fold. Once again, a larger effect is observed in the value of Kis for MMP, which increases by 120-fold. While a 2-fold increase is observed in the value of Km for NAD+, the value of Kii for TAD decreases 5-fold. No NAD+ substrate inhibition is detected, in keeping with the decrease in kcat. Like Asp13, we tentatively assign Asp50 to a monovalent cation binding site since the largest effect (not including MMP affinity) is on K+ activation.

Asp248Ala. The Asp248 f Ala mutation causes a 130fold decrease in the value of kcat. In addition, the value of Kii for TAD increases by 25-fold, and the value of Km for NAD+ increases by 3-fold. This mutation also increases the value of Km for K+ by 13-fold. No NAD+ substrate inhibition is detected, again in keeping with the decrease in kcat. While a 3-fold decrease is observed in the value of the Km for IMP and a 4-fold decrease in the Kis for XMP, no change in the Kis for GMP is observed. Once again, a greater perturbation is observed in the value of the Ki for MMP, which increases by 80-fold. We assign this residue to the NAD+ site, since this mutation causes a large decrease in the value of kcat and a substantial increase in the value of Ki for TAD, while smaller changes are observed in the values of Ki for IMP analogs. Asp338Ala. While another laboratory was unable to detect activity in the analogous mutant of Chinese hamster IMPDH (Sintchak et al., 1996), we can detect activity in Asp338Ala mutant of E. coli IMPDH. This activity is not the result of wild-type contamination: a greater than 103-fold increase in the value of Ki for MMP is observed and EICARMP does not rapidly inactivate Asp338Ala as seen with wild-type enzyme. The Asp338 f Ala mutation has a large effect on the value of kcat, which decreases by 600-fold. The Asp338 f Ala mutation increases the value of Km for IMP by 12fold and the values of Kis for GMP and XMP by approximately 6-fold. No change in the value of Km for NAD+ is observed. A 6-fold increase in the value of Km for K+ is also noted. The large change in the value of kcat and the smaller changes in the values of Km for IMP and Kis for XMP and GMP indicate that Asp338 may be an acid-base catalyst in the IMP binding site. Glu469Ala. The Glu469 f Ala mutation increases the value of Km for K+ by 17-fold. The only other change observed is in the value of Km for NAD+, which increases by 5-fold. This mutation does not affect the values of kcat and Km for IMP, the value of Kii for NAD+ substrate inhibition, or the value of Kii for TAD. These observations suggest that Glu469 is near a K+ binding site. However, the failure to observe a change in kcat suggests that Glu469 is probably not a ligand for K+. MMP Inhibition. As mentioned above, much larger increases were observed in the values of Ki for MMP than in the values of Km for IMP or Kis for GMP and XMP. The increases in the values of Ki for MMP appeared to correlate with decreases in values of kcat. This observation suggests

Conserved Carboxylate Residues in IMPDH

FIGURE 6: Correlation of Ki and kcat/Km*Km values. Kis GMP (O), Kis XMP (]), Ki MMP (b). Lines are from linear regression analysis.

that MMP may be a transition state analog of the IMPDH reaction. Such a transition state analogy can be confirmed by demonstrating that the values of Ki correlate with the values of kcat/Km for a series of analogous substrates and inhibitors (Wolfenden, 1969; Bartlett & Marlowe, 1983). Alternatively, a correlation between the values of Ki and kcat/ Km for a single substrate/inhibitor pair and a series of mutant enzymes can be used (Phillips et al., 1992). For a bisubstrate enzyme such as IMPDH, the affinity of a transition state analog will correlate with kcat/KmKm (Wolfenden, 1969). In order to test the transition state analog hypothesis, the Ki of MMP was plotted versus kcat/KmKm for each of the mutant enzymes (Figure 6). A good correlation is observed (r2 ) 0.9) with a slope of 0.8. No such correlation is observed for the values of Kis for GMP and XMP (r2 ) 0.2 and 0.1, respectively) (Figure 6) or the Kii for TAD or when the Ki for MMP is plotted against Km for IMP (data not shown). DISCUSSION Comparison with the Crystal Structures of IMPDH. We have assigned functions to five IMPDH residues: Asp13, Asp50, and Glu469 are involved in K+ binding; Asp13 and Asp50 are possible ligands at a K+ binding site, Asp248 is involved in NAD+ binding and Asp 338 is a likely general acid-base catalyst at the IMP binding site. In addition, we found that the mutation of Glu54, Asp138, Asp200, Asp243, Glu369, and Glu373 have only minor effects on IMPDH function. The recent reports of crystal structures of IMPDH allow us to map some of these residues onto the protein structure. Three crystal structures of IMPDH have been solved: the E-XMP*‚MPA complex of IMPDH from Chinese hamster (Sintchak et al., 1996) and the apoenzyme and E‚XMP complex of Tritrichomonas foetus IMPDH (Whitby et al., 1997). The coordinates of T. foetus IMPDH were generously provided prepublication, while the coordinates of Chinese hamster IMPDH are not yet available. Both groups report that IMPDH has an R/β barrel structure. Common to R/β barrel proteins, the active site of IMPDH is composed of loops C-terminal to the β strands of the barrel (Farber & Petsko, 1990). The loop after β8 forms a flap which covers the active site. Similar flaps control access to the active sites in other R/β barrel proteins (Joseph et al., 1990). In addition,

Biochemistry, Vol. 36, No. 43, 1997 13371 IMPDH contains an unique 150 residue insertion between R2 and β3. This “subdomain” is missing in IMPDH from Borrelia burgdorferi (Zhou et al., 1997). Sintchak et al. (1996) report that the subdomain can be deleted without loss of IMPDH activity, although no details of this experiment have been presented. Thus, the subdomain is not required for IMPDH activity. The active site is adjacent to the subunit interface and near the N- and C-termini of the neighboring subunit in the tetramer. Unfortunately, both structures contain large regions of disorder, including portions of the flap, the subdomain and the N- and C-termini. Much of the active site of T. foetus IMPDH is also disordered, including the active site Cys. The six residues which are not required for IMPDH activity should be located far from the active site. Indeed, two of these residues, Asp138 and Asp200, are found in the subdomain, and another, Asp243, is found on the N-terminal end of the β barrel and, thus, far from the active site. Although Glu369 and Glu373 are in the C-terminal loops of the β sheets, they are nevertheless at least 16 Å from XMP in the structure of T. foetus IMPDH. Therefore, five of the residues which are not required for IMPDH activity are all located far from the active site. However, Glu54 is also found in the C-terminal loops; the analogous residue, Gly64, is 12 Å from XMP in T. foetus IMPDH, which suggests that the side chain of Glu54 could be quite close to the active site. The failure to observe a significant effect for this mutation is somewhat surprising. Asp248 Is in the NAD+ Site. The Asp248 f Ala mutation causes a 25-fold increase in the value of Kii for TAD and a 120-fold decrease in the value of kcat, which suggests that Asp248 is in the NAD+ site. Asp248 is found in the MPA binding site of IMPDH (Sintchak et al., 1996), and MPA is known to bind in the nicotinamide portion of the NAD+ binding site (Hedstrom & Wang, 1990). Therefore, both mutagenesis and structural data suggest that Asp248 is in the NAD+ binding site. Asp338 May be a General Acid-Base Catalyst. The Asp338 f Ala causes the greatest decrease in kcat (600-fold). This change is accompanied by comparatively modest increases in the values of Km for IMP and Kis for GMP and XMP (e12-fold). These observations suggest that Asp338 contributes more to catalytic activity than substrate binding. Thus, it is tempting to propose that Asp338 acts as a general acid-base in the IMPDH reaction. However, Asp338 makes hydrogen bonds to the 2′ and 3′ hydroxyls of both E-XMP* and E‚XMP (Sintchak et al., 1996; Whitby et al., 1997). Presumably, Asp338 makes these same interactions with IMP, which would seem to prevent this residue from acting as a general acid-base. However, Asp338 appears to be linked to N3 of E-XMP* by a network of bound water molecules. It is intriguing to speculate that Asp338 acts as a general acid or base via this water network. Alternatively, Asp338 may have a different orientation in the E‚IMP complex. Indeed, the conformation of enzyme bound IMP is different than E-XMP*: enzyme-bound IMP has a C2′endo ribose conformation whereas E-XMP* has a C3′-endo conformation (Xiang & Markham, 1996). Experiments are in progress to further delineate the role of Asp338 in the IMPDH mechanism. MonoValent Cation ActiVation of IMPDH. Mutations of the remaining three residues, Asp13, Asp50, and Glu469, appear to exert their effects primarily through K+ binding.

13372 Biochemistry, Vol. 36, No. 43, 1997 The mutation of both Asp13 and Asp50 decrease the value of kcat as well as the affinity for K+. Therefore, we believe that both Asp13 and Asp50 could be ligands at the K+ binding site. In contrast, the mutation of Glu469 does not decrease kcat, although this mutation increases the value of Km for K+ by 17-fold. Therefore, it is likely that Glu469 interacts with the ligands of the K+ site. Most monovalent cation binding sites contain an Asp or Glu residue (Toney et al., 1993; Larsen et al., 1994; Liaw et al., 1995; Koster et al., 1996). However, alkali metal binding sites are extremely difficult to identify crystallographically. Unfortunately, the IMPDH structures provide limited insight into monovalent cation activation. No monovalent cation sites were located in the T. foetus structure, in keeping with the its low dependence on monovalent cations. Intriguingly, Asp50 is substituted with Gln in T. foetus IMPDH. While Sintchak et al. (1996) claim to identify a monovalent cation binding site in Chinese hamster IMPDH, only one ligand, the carbonyl of the active site Cys, was specified. The remaining ligands include four main chain carbonyls, three of which are somewhere in the C-terminal region, and a water molecule. Thus, neither Asp13 nor Asp50 appear to be ligands at this site, although it is possible that Glu469 is nearby. Unfortunately, Glu469 is disordered in the crystal structure of T. foetus IMPDH. However, both Asp13 and Asp50 are discernible (Whitby et al., 1997). Asp13 is located in the subunit interface while Asp50 is near the active site; these two residues are separated by at least 30 Å across the monomer or the nearest subunit. Therefore, it is likely that Asp13 and Asp50 demarcate two distinct K+ binding sites. Transition State Analogy of MMP. MMP is the active metabolite of the immunosuppressive agent mizoribine and a potent inhibitor of IMPDH. In the course of these experiments we noticed that the mutations have a much greater effect on the value of the Ki for MMP than on the Ki of the other IMP analogs. Moreover, the changes in the values of Ki for MMP correlate with the changes in the values of kcat/KmKm (Figure 6). This observation identifies MMP as a transition state analog for the IMPDH reaction. No such correlation is observed for the values of Kis for GMP and XMP or Kii for TAD, indicating that these compounds are ground state analogs, as expected. The slope of the correlation is 0.8; this slope may indicate that MMP recapitulates 80% of transition state character. It seems likely that the negative charge of MMP mimics the charge which develops on N3 of IMP during the IMPDH reaction (Figures 1 and 2). Conclusions. We identified five functionally important Asp/Glu residues in E. coli IMPDH: Asp248 is involved in NAD+ binding, Asp338 may be an acid-base catalyst, Asp13 and Asp50 may be ligands at two distinct K+ binding sites, and Glu469 is near a K+ binding site. In addition, we demonstrate that MMP is a transition state analog for the IMPDH reaction. ACKNOWLEDGMENT We would like to thank Geoff Stamper for initiation of the EDC work, Joyce Keck for her work on the K+ dependence of wild-type and the Asp50Ala mutant, and Frank Whitby and C. C. Wang for generously providing the coordinates of the T. foetus structure. Special thanks go to Rebecca Myers for the DNA sequencing of all mutants and

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